Many techniques in modern biology require nucleic acid amplification as an initial step. As just a few examples, DNA cloning, DNA fingerprinting, sequencing, and molecularly-based disease detection and diagnosis often rely on amplification of the nucleic acid target of interest. The polymerase chain reaction (PCR) is widely used for nucleic acid amplification and has been successfully employed to amplify a variety of nucleic acid targets. However, PCR is not ideal for amplification of all possible targets.
In particular, PCR amplification of targets containing short repeated sequences (e.g., dinucleotides, trinucleotides, etc.) can be hampered by problems such as stutter. A stutter product is a PCR artifact that is one or more repeat units shorter or longer than the original target sequence. Stutter products typically increase in quantity as the length of the target sequence increases, and can introduce uncertainty into attempts to determine copy number of such repeated sequences. Additionally, palindromic sequences and sequences with extreme GC content are difficult and sometimes impossible to amplify.
Methods for amplifying nucleic acid targets, including targets containing repeated sequence elements, are thus desirable. The present invention meets these and other needs by providing, inter alia, methods and compositions for nucleic acid amplification. A complete understanding of the invention will be obtained upon review of the following.